Hi Donald
Thanks for that. That was my original thought - that I'd have to run them
separately and look at effects of condition and time. I'll give these a
go.
Prapti
On 2/10/12 3:27 PM, "MCLAREN, Donald" <[log in to unmask]> wrote:
>I would run 4 models. Each model will have 7 subjects and 1 image per
>subject. It will be a two-sample t-test.
>
>Each image will be the difference of time1 and time2 for each of your
>four conditions, hence the four models.
>
>In setting up the model for each condition and using the difference
>images, you can use FEAT and randomise.
>
>If you were to setup a big model with all conditions, two groups, and
>two timepoints, you'd have at least two problems:
>(1) you'd have poor estimates of the effects since you have multiple
>within-subject factors that increase the probability of violations of
>sphericity, which are not corrected in FSL; and (2) you wouldn't be
>able to use randomise. Thus, simplifying the model to a series of
>paired t-tests since your not looking at the group*time*condition
>interactions is probably your best option for the group models.
>
>
>Best Regards, Donald McLaren
>=================
>D.G. McLaren, Ph.D.
>Postdoctoral Research Fellow, GRECC, Bedford VA
>Research Fellow, Department of Neurology, Massachusetts General Hospital
>and
>Harvard Medical School
>Office: (773) 406-2464
>=====================
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>On Fri, Feb 10, 2012 at 6:10 PM, Gautam, Prapti <[log in to unmask]>
>wrote:
>>
>> The 4 copes are each different conditions in a task and I want to look
>>at
>> them separately. Yes, there are two time points.
>>
>> Prapti
>>
>> From: Jeanette Mumford <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Date: Fri, 10 Feb 2012 17:07:23 -0600
>>
>> To: <[log in to unmask]>
>> Subject: Re: [FSL] help with design matrix-longitudinal study
>>
>> What are your 4 copes? How many time points are there, two? Are you
>>trying
>> to relate these 4 copes to each other or are you looking at each one
>> separately?
>>
>> Jeanette
>>
>> On Fri, Feb 10, 2012 at 12:28 PM, Gautam, Prapti <[log in to unmask]>
>> wrote:
>>>
>>> Hi Jeanette,
>>>
>>> Thank you for the link. However, I am really new at this, and I still
>>>have
>>> a few more questions.
>>> The model in the example seems to refer to mean group differences
>>>between
>>> the two groups. While I am interested in that, I would also like to
>>> investigate differences between different task levels with time for
>>>which I
>>> am currently using four copes in the first level analyses. Do you know
>>>how I
>>> would accommodate these copes in the design matrix and look for
>>>differences
>>> between the two groups as well as looking at change with time ? Or
>>>should
>>> these be two different types for analyses? One for group differences
>>>and one
>>> for time point differences?
>>>
>>> Thanks,
>>>
>>> Prapti
>>>
>>>
>>> From: Jeanette Mumford <[log in to unmask]>
>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>> Date: Thu, 9 Feb 2012 17:09:57 -0600
>>> To: <[log in to unmask]>
>>> Subject: Re: [FSL] help with design matrix-longitudinal study
>>>
>>> I think you'd follow the model described here:
>>>
>>>
>>>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0809&L=fsl&P=R7901&1=f
>>>sl&9=A&J=on&K=2&d=No+Match%3BMatch%3BMatches&z=4
>>>
>>>
>>> Hope that helps,
>>> Jeanette
>>>
>>> On Thu, Feb 9, 2012 at 4:44 PM, Gautam, Prapti <[log in to unmask]>
>>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I am trying to design a longitudinal experiment looking at group
>>>> differences over 2 time points but I am having trouble designing the
>>>> contrasts and the design matrices.
>>>>
>>>> For example, if I had 3 patients and 4 controls in the study, I think
>>>> that I can conduct the first and second level analyses separately for
>>>>the
>>>> two groups and then find group level differences in the third level
>>>> analyses. For the analyses, I would have 4 copes for the first level,
>>>>which
>>>> could then be fed into the second level, the results of which would
>>>>then be
>>>> fed into the third level.
>>>>
>>>> However, I am not too sure whether this would be the best way to do
>>>>the
>>>> analyses. I have looked at the examples in the FSL pages for help with
>>>> higher level analyses, but I couldn't figure out if the examples
>>>>applied to
>>>> my case.
>>>>
>>>> If I could get some advice on how to set up the design matrices and
>>>>the
>>>> contrasts, that would be very helpful,
>>>>
>>>> Thanks,
>>>>
>>>> Prapti
>>>>
>>>>
>>
>>
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